The 34-year-old submarine had gone through a refit and was "in perfect condition," Macri told reporters at the Argentine navy headquarters.
"My commitment is with the truth," he said, adding the tragedy "will require a serious, in-depth investigation that will yield certainty about what has happened."
Argentina's navy has been fiercely criticized for its handling of the operation since first reporting the submarine overdue at its Mar del Plata base on November 16.
Only on Thursday did the navy confirm there had been an explosion on board, which experts said was likely linked to the battery problem.
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"Until we have the complete information, we do not have to look for the guilty, to look for those responsible. First we have to have certainty of what happened and why it happened," said Macri.
The center-right leader spoke as the search for the San Juan shifted from rescue to recovery yesterday, after navy officials lost hope of finding alive any of the crew, which included the country's first female submarine officer.
Magistrate Marta Yanez has already begun preliminary investigations into the disaster.
She told reporters that unlike a plane, "the submarine does not have a black box. The black box is the submarine," and it would have to be recovered before the causes of the explosion could be known.
Officially the navy has not declared the loss of the crew, but marine experts believe an explosion would have been catastrophic.
Brenda Salva, a friend of crew member Damian Tagliapietra, said she had been told by the commander of the Mar del Plata naval base: "They are all dead."
A second sailor, aged 26, had been ready to join the ill- fated sub but was exempted because he was finalizing the purchase of a house, the Clarin newspaper reported.
For the relatives of the crew, grief turned to anger.
"I want to tell Admiral Marcelo Srur that he is not in a position to be in charge of a force, and to the president (Mauricio Macri), to bring order," said Maria Rosa Belcastro, mother of 38-year-old Lieutenant Fernando Villarreal.
In his comments at the navy headquarters, Macri paid tribute to the "patriotism, heroism and bravery" of the San Juan's crew.
"For all of them and their families, my greatest affection," he said.
To the relatives of the missing submariners he said: "The pain is great but we are together, and we are going to travel this road all the way together.